HIBAG

DOI: 10.18129/B9.bioc.HIBAG    

HLA Genotype Imputation with Attribute Bagging

Bioconductor version: Release (3.12)

Imputes HLA classical alleles using GWAS SNP data, and it relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.

Author: Xiuwen Zheng [aut, cre, cph] , Bruce Weir [ctb, ths]

Maintainer: Xiuwen Zheng <zhengx at u.washington.edu>

Citation (from within R, enter citation("HIBAG")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HIBAG")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HIBAG")

 

HTML R Script HIBAG algorithm implementation
HTML R Script HIBAG vignette html
HTML R Script HLA association vignette html
PDF   Reference Manual
Text   NEWS

Details

biocViews Genetics, Software, StatisticalMethod
Version 1.26.0
In Bioconductor since BioC 3.1 (R-3.2) (5.5 years)
License GPL-3
Depends R (>= 3.2.0)
Imports methods, RcppParallel
LinkingTo RcppParallel
Suggests parallel, knitr, gdsfmt, SNPRelate, SeqArray, ggplot2, reshape2
SystemRequirements C++11, GNU make
Enhances
URL http://github.com/zhengxwen/HIBAG https://hibag.s3.amazonaws.com/index.html http://www.biostat.washington.edu/~bsweir/HIBAG
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HIBAG_1.26.0.tar.gz
Windows Binary HIBAG_1.26.0.zip
macOS 10.13 (High Sierra) HIBAG_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HIBAG
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HIBAG
Package Short Url https://bioconductor.org/packages/HIBAG/
Package Downloads Report Download Stats

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